[Gate-users] Position Voxel PET Source on top of DICOM CT

[BAKER, Mark (THE CLATTERBRIDGE CANCER CENTRE NHS FOUNDATION TRUST)]

Hi all

I'm really struggling with my current macro, in which I am aiming to position a F18 PET image as a voxelised source on top of a CT image. I have two sets of data at the moment, a patient image and a NEMA phantom image. With the NEMA phantom image, when observing the geometry using OGL, my trajectories appear to come from what I think is too far a negative z-direction (assuming the axis from the visualisation is pointing in a positive direction) i.e. almost the edge of the world and definitely outside of the CT phantom image. With the patient image, the source distribution does overlay the CT information, but it is flipped such that the head is in the pelvis region and vice versa.

My best guess is that the orientation or offset of either setup is incorrect. The CT dataset originally started as set as 0 translation in all directions, with no rotation axis or angle, and the source position set as negative half of the PET image size (e.g. -400 -400 -170 mm) - this is what I understand as to how the images should be arranged. However, I have tried all sorts of combinations of rotations, translations and source positions (including some wild numbers just to see if they make any impact) but they don't change what I'm seeing. I get the same effect whether the images are DCM or MHD (albeit converted from DCM to MHD using ImageJ).

I've attached all three relevant macs to this email. To actually run Gate, I use a script to pass variables into 8  instances of Gate in order to utilise the 8 cores on the machine.  Only main1.mac contains instructions to open the visualisation (as main2-8 are exact copies, there is no need to duplicate resource demand).

I'm sure I am just missing something really obvious, but I'd appreciate if anyone could help me out.

Additionally, whether this is related or not, but when I first open the terminal and run my macro, I can almost guarantee that the process will hang on deleting the visualisation manager the first time it is run. I can CTRL-C and then re-run the exact same script, and it proceeds fine. It only started doing this pretty recently, and I'm not sure what I have done differently to cause this. It might possibly be linked, or might be a total red herring.

Thank you

Mark Baker
Principal Clinical Scientist
Imaging Physics (Ionising)
The Clatterbridge Cancer Centre NHS Foundation Trust
(he, him)

CCCW Tel:  0151 556 5030
CCCL Tel: 0151 318 8438
Email: mark.baker23 at nhs.net<mailto:mark.baker23 at nhs.net>
Microsoft Teams (click here)<https://teams.microsoft.com/l/chat/0/0?users=mark.baker23@nhs.net>

Honorary Lecturer, Dept. of Physics
University of Liverpool

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